Computational protocol: C1q Deficiency and Neuropsychiatric Systemic Lupus Erythematosus

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Protocol publication

[…] Genomic DNA was extracted from blood collected with tubes supplemented with EDTA. Sequencing of the complete C1q genes (C1qA, C1qB, and C1qC), of both introns and exons was performed as before (). Deep-sequencing was performed using the 454 NGS Roche GS FLX Titanium platform. Data were compared to internal controls and to Human Genome build 19 as well as Human_v37_2 de dbSNP database v132 using the NextGENe software package for Next Generation Sequence Analysis (NGS) from Softgenetics. The effect of the mutation on splicing was in silico analyzed using the NetGene2 Server, http://www.cbs.dtu.dk/services/NetGene2/. […]

Pipeline specifications

Software tools NextGENe, NetGene2
Databases dbSNP
Application WGS analysis
Organisms Homo sapiens
Diseases Deficiency Diseases, Galactosemias, Immunologic Deficiency Syndromes, Lesch-Nyhan Syndrome, Lupus Erythematosus, Systemic, Vasculitis, Central Nervous System, Lupus Vasculitis, Central Nervous System